Abstract: The extraction efficiency of coalbed methane is affected by many factors. Among them, the fracturing fluid injected during coal seam mining and indigenous liquid water in the coal seam often hinder the diffusion and exploitation of coalbed methane, which leads to the water block effect (WBE). The cause, mechanism, and mitigation methods of the WBE are still not completely understood, and are also the topics of current research. This study was based on a large-scale molecular model which accurately reflects the chemical structure of coal, this study used molecular dynamics (MD) methods to simulate the flow patterns of methane and water in the micro-pores of coal seams, considering the hindering effect of water film on methane. The impact of factors such as water film thickness, pore size, reservoir pressure, and pressure difference on the transport velocities of methane and water film has been quantitatively calculated. The results demonstrate that the existence of water will significantly hinder the diffusion of methane and cause WBE. The pore size and pressure drop will also affect the two-phase flow speed of methane and water. Larger pore size and higher pressure drop favor the flow of methane and water. Through analyzing the structural changes of the water film during its transportation, the patterns of occurrence and disappearance of WBE was investigated. Under the conditions of larger pore sizes and thicker water films, the water phase can maintain a continuous phase during the flow process, which completely seal the pores in the coal seam, and cause the WBE. On the other hand, when the water film is thin or the pore size is small, the attractive interaction between water molecules and coal seam makes it easier for the water phase to break into multiple water molecular clusters and mix with the methane gas phase, thus alleviating the WBE. Based on the nano-scale molecular models, this study quantitatively investigated the effects of pore sizes, pressures differences, and water film on WBE, showing that reducing the interactions between water molecules while enhancing the attraction between water and coal may alleviate WBE. This study can provide some insights on further understanding the mechanisms of WBE and improving the recoverying efficiency of coalbed methane.